This thesis presents a new modeling framework and research methodology for the study of engineering systems. The thesis begins with a formal conceptualization of Engineering Systems based upon a synthesis of various literatures. Using this conceptualization, a new modeling framework is presented called the Engineering Systems Matrix (ESM). The ESM is an improvement to existing system-level modeling frameworks, such as the Design Structure Matrix (DSM), by providing a dynamic, end-to-end representation of an engineering system. In support of this contribution, a new research methodology is presented called Qualitative Knowledge Construction (QKC). QKC can be thought of as a Bayesian-type approach to grounded theory. The methodology integrates qualitative social science with quantitative methods by developing a procedure for translating textual reports of observations, interview transcripts, system documentation, and figures into coded data represented in the ESM. The thesis develops the ESM framework and the QKC methodology in the context of a real world engineering system, a US Air Force miniature uninhabited air vehicle (MAV) product development system.